Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagttccttttgctaattggtgcctttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcag

Basic information

species Zea mays
transcript GRMZM2G011518_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011518_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os10g42940.1 (Oryza sativa), 5'ss of exon 4
ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttg--------------tagttccttttgc--taattggtgcct--ttgtgcactgagcttctatgtaatatctactctaacttgttttgaaattttaaatctctttcag
|| ||||| |||||||| |||||||||||||| || ||||||||||| || || ||||||||||               || ||  || ||    |    |||  |  || ||||||||  ||   ||   | | | |||||||||  | ||   |  |   | ||||||||
ATCTACGTAGTTGATTCCCTGGATAGAGAGAGGATTGGGAGAGCCAGAGCTGAATTTCAGgtttacatatatgtataaataatttattatgaggcagcaagtgtttgcttctgcactgacatttgttgccttgt-tgctctaacttactgtgtggtaatc--tgtctttcag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|60357839|gb|DN224812.1|DN224812
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|76285293|gb|DV024861.1|DV024861
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|60394445|gb|DN227315.1|DN227315
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|78021761|gb|DV490148.1|DV490148
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|60337699|gb|DN204672.1|DN204672
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|166598077|gb|EG306730.1|EG306730
EST:     CCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: CCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|76010832|gb|DT938002.1|DT938002
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
EST: gi|60399444|gb|DN232256.1|DN232256
EST:     TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAG                         GCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT
genomic: TTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 92

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG


Block sizes: 49 (upstream exon), 44 (downstream exon)
Score: 80

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 119

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 81

ATTTACGTGGTTGATTCACTGGATAGAGAGAGAATCGGGAGAGCCAGGGCGGAGTTTCAGgtttgtagtt ... tctctttcagGCTATAATCAATGACCCTTTTATGCTTAACAGTGTGTTATTGGTGTTTGCTAACAAGCAAGACATG